The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'prepGWAS_shah'
Caused by:
Process `prepGWAS_shah` terminated with an error exit status (1)
Command executed:
module load gcc/11.4.0 openmpi/4.1.4 R/4.3.1
# Run analysis script
Rscript /standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/scripts/standardize_GWAS_eQTL_for_coloc_new.R \
--gwas ShahS_31919418_HeartFailure.gz \
--prefix shah20_gwas_HF \
--liftover TRUE
Command exit status:
1
Command output:
[1] "Finished standardizing columns"
[1] "Processing LiftOver!"
Command error:
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:lubridate’:
%within%
The following objects are masked from ‘package:dplyr’:
collapse, desc, slice
The following object is masked from ‘package:purrr’:
reduce
The following object is masked from ‘package:data.table’:
shift
Loading required package: GenomeInfoDb
Discarding unchained sequences: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 5, 6, 7, 8, 9, 1, 2, 3, 4
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘XVector’
The following object is masked from ‘package:purrr’:
compact
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Error: object 'gwasTest' not found
Execution halted
Work dir:
/sfs/ceph/standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/work/14/54e4fd2773cdbd346aa6036630fa63
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
nextflow run main_process.nf -profile slurm -resume -bgec6934758e438790c048328bdca43b36a324e47c-2917-4670-abd9-b331a64efb5bThese plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.